The Red-crowned Crane Grus japonensis is an endangered species that has two separate breeding populations, one in the Amur River basin and the other in north and east Hokkaido, Japan. So far, only two (Gj1 and Gj2) and seven (Gj3-Gj9) haplotypes in D-loop of mtDNA were identified in Japan and in the continent, respectively. We obtained feathers from three cranes found in northeast Honshu. The crane in Akita in 2008, which also arrived at west Hokkaido, had a novel haplotype (Gj10). Another crane in Akita in 2009 showed a heteroplasmy (Gj7 and a novel type, Gj12). The third crane in Miyagi in 2010 also showed another type, Gj11. These results suggest that three Red-crowned Cranes appeared in Honshu and west Hokkaido were from the continent.